After a goalless opening 45 minutes the Glovers dominated proceedings in the second half, hitting the crossbar twice and peppering the Bees goal.
With Town deserving to make it three months unbeaten at home they were dealt a sucker punch with a little over five minutes remaining when Alex Nicholls found the back of the net during a rare foray into Yeovil’s half.
Otis Khan was denied late on as the Glovers piled numbers forward, but Darren Way’s side couldn’t find an equaliser and lost their first match in League Two since October 1st.
After making four changes in midweek for the Checkatrade Trophy, Way reverted to the side that saw off Crawley Town 5-0 at Huish Park last weekend in Sky Bet League Two, with Artur Krysiak, Alex Lawless, Otis Khan and Tom Eaves all returning to the starting eleven.
With nine goals netted in their previous two matches on home soil the Glovers immediately looked to get back on the goal trail, producing the first chance of the game with just four minutes on the clock.
Swansea loanee Ryan Hedges danced past three Bees defenders to engineer space on the edge of the box, with his well-struck effort from 20 yards being pushed over the bar by visiting ‘keeper Jamie Stephens.
Looking most threatening down the wings Otis Khan on the other side soon tested Stephens, cutting inside before seeing his effort comfortably collected at the near post.
Rossi Eames’ side steadied the ship after a bright start from the hosts, with the first half becoming a scrappy affair with Barnet happy to make it a stop-start clash at Huish Park.
Fifteen goal striker John Akinde was Barnet’s focal point in attack, but the 27-year-old endured a frustrating opening 45 minutes which resulted in the former Bristol City striker going into the referee’s book for a late challenge on Hedges.
With neither side able to engineer much by way of goal scoring opportunities, an off target effort from Tom Gambin and a dipping Ryan Dickson volley was as good as it got in a tepid first half in Somerset.
Neither manager made a change of personnel at the break but it was the Glovers who started the brighter once again.
After good hold-up play from Eaves, Dickson laid the ball off for Kevin Dawson whose deflected effort from 25 yards was pushed behind by Stephens.
Town continued to press and went even closer just before the hour mark when Dickson’s cross caused chaos in the Barnet box.
Stephens couldn’t claim the ball under pressure from Nathan Smith allowing Eaves to instinctively head at goal from inside the box, but the frontman’s effort came back off the bar.
That buoyed both the home crowd and Way’s side, who engineered another opportunity a minute later with Ben Whitfield prodding an effort into the side-netting from the angle.
Having found their feet in the final third Yeovil continued to carve open the Bees, with Khan having a shot destined for the bottom corner deflected behind by visiting captain Michael Nelson.
Entrenching themselves in the Barnet half Dickson glanced Dawson’s cross just wide, before a number of Hedges deliveries caused chaos in the box with Stephens increasingly uncertain.
Way introduced Francois Zoko with 20 minutes remaining with Town looking to make it three victories in a week at home, but it was Khan who went close with the latest Glovers attempt.
Lawless’ superb angled cross was knocked down by Eaves to the wideman on the edge of the box, with Khan’s well-hit strike coming back off the crossbar once again.
Barnet dropped deeper and deeper but almost caught Town on the break when Akinde charged through on goal, only for Krysiak to race from his line and smother the ball.
With Yeovil searching for a deserved goal it was the visitors who dealt a sucker punch with six minutes of normal time remaining.
Curtis Weston won possession deep in the Yeovil half and found substitute Alex Nicholls wide inside the box, with the winger picking out the bottom corner to give Barnet the lead completely against the run of play.
Way’s side threw everything forward in a bid to get something from a game they deserved to win, but Stephens produced a superb save in the 90th minute to deny Khan after he raced through on goal.
That was the closest Yeovil came to levelling the scores late on as Barnet held firm, to condemn Town to a first defeat in the league since the start of October and a first loss at home since the 10th September.
Yeovil Town: Krysiak; Shephard, Lacey, Smith, Dickson; Dawson, Lawless, Whitfield (Zoko 69’); Hedges, Eaves (Campbell 82’), Khan.
Subs not used: Maddison, Mugabi, Ezewele, Butcher, Sowunmi.
Barnet: Stephens; Taylor, Nelson, Dembele, Johnson; Vilhete, Weston, Champion (Nicholls 60’), Gambin (Muggleton 82’); Mason-Clark (Akpa Akpro 66’); Akinde.
Bookings: Akinde 27’, Dembele 34’, Johnson 85’.
Subs not used: Vickers, Sesay, Watson, Kyei.